Rodrigo Costa
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View article: An artificial selection procedure enriches for known and suspected chitin degraders from the prokaryotic rare biosphere of multiple marine biotopes
An artificial selection procedure enriches for known and suspected chitin degraders from the prokaryotic rare biosphere of multiple marine biotopes Open
Background Biological chitin degradation is a major process in the ocean, governed primarily by the action of microorganisms. It is known that the structure and taxonomic profile of chitin-degrading microbial communities change across mari…
View article: A genomic view of the bacterial family Endozoicomonadaceae in marine symbioses
A genomic view of the bacterial family Endozoicomonadaceae in marine symbioses Open
Endozoicomonadaceae bacteria are found in association with marine organisms across ocean ecosystems. Interactions may range from mutualistic to parasitic depending on host species and ecological context. Their genomic repertoire suggests m…
View article: Selective shaping of prokaryotic communities and core symbiont maintenance suggest large-scale aquarium facilities as reservoirs of microbiome diversity in octocorals
Selective shaping of prokaryotic communities and core symbiont maintenance suggest large-scale aquarium facilities as reservoirs of microbiome diversity in octocorals Open
Introduction Octocorals play a critical role in coral ecosystems, contributing to habitat complexity and marine biodiversity. Despite their ecological importance, the microbial communities associated with octocorals remain understudied, pa…
View article: The chromosomal genome sequence of the elephant ear sponge, Spongia lamella (Schulze, 1879), and its associated microbial metagenome sequences
The chromosomal genome sequence of the elephant ear sponge, Spongia lamella (Schulze, 1879), and its associated microbial metagenome sequences Open
We present a genome assembly from a specimen of Spongia lamella (Elephant ear; Porifera; Demospongiae; Dictyoceratida; Spongiidae). The genome sequence has a total length of 130.43 megabases. Most of the assembly (98.43%) is scaffolded int…
View article: Genome sequence of the marine bacterium <i>Roseobacter</i> sp. EG26, isolated from the octocoral <i>Eunicella gazella</i> , suggests aptitude for a host-associated lifestyle
Genome sequence of the marine bacterium <i>Roseobacter</i> sp. EG26, isolated from the octocoral <i>Eunicella gazella</i> , suggests aptitude for a host-associated lifestyle Open
We present the genome sequence of the octocoral-associated Roseobacter sp. EG26. We highlight features related to type II, III, IV, and VI secretion systems, ankyrin-repeat proteins, and taurine degradation, suggesting a preference for a h…
View article: Endozoicomonas lisbonensis sp. nov., a novel marine bacterium isolated from the soft coral Litophyton sp. at Oceanário de Lisboa in Portugal
Endozoicomonas lisbonensis sp. nov., a novel marine bacterium isolated from the soft coral Litophyton sp. at Oceanário de Lisboa in Portugal Open
This study describes a Gram-stain-negative, rod-shaped, facultatively anaerobic bacterial species isolated from the octocoral Litophyton sp. inhabiting the live coral aquarium at Oceanário de Lisboa in Portugal. Four strains, NE35, NE40 T …
View article: An artificial selection procedure enriches for known and suspected chitin degraders from the prokaryotic rare biosphere of multiple marine biotopes
An artificial selection procedure enriches for known and suspected chitin degraders from the prokaryotic rare biosphere of multiple marine biotopes Open
Background Biological chitin degradation is a major process in the ocean, governed primarily by the action of microorganisms. It is now known that the structure and taxonomic profile of chitin-degrading microbial communities change across …
View article: Genome sequences of four novel <i>Endozoicomonas</i> strains associated with a tropical octocoral in a long-term aquarium facility
Genome sequences of four novel <i>Endozoicomonas</i> strains associated with a tropical octocoral in a long-term aquarium facility Open
We report the genome sequences of four Endozoicomonas sp. strains isolated from the octocoral Litophyton maintained long term at an aquarium facility. Our analysis reveals the coding potential for versatile polysaccharide metabolism; Type …
View article: Genome sequence of the marine alphaproteobacterium <i>Lentilitoribacter</i> sp. EG35 isolated from the temperate octocoral <i>Eunicella gazella</i>
Genome sequence of the marine alphaproteobacterium <i>Lentilitoribacter</i> sp. EG35 isolated from the temperate octocoral <i>Eunicella gazella</i> Open
We report the genome sequence of Lentilitoribacter sp. strain EG35 isolated from the octocoral Eunicella gazella sampled off the coast of Portugal. We reveal the coding potential for the biosynthesis of polyhydroxyalkanoates — biodegradabl…
View article: Selection of marine bacterial consortia efficient at degrading chitin leads to the discovery of new potential chitin degraders
Selection of marine bacterial consortia efficient at degrading chitin leads to the discovery of new potential chitin degraders Open
Chitin degradation is a keystone process in the oceans, mediated by marine microorganisms with the help of several enzymes, mostly chitinases. Sediment, seawater, and filter-feeding marine invertebrates, such as sponges, are known to harbo…
View article: Full-length 16S rRNA gene sequencing combined with adequate database selection improves the description of Arctic marine prokaryotic communities
Full-length 16S rRNA gene sequencing combined with adequate database selection improves the description of Arctic marine prokaryotic communities Open
Background High-throughput sequencing of the full-length 16S rRNA gene has improved the taxonomic classification of prokaryotes found in natural environments. However, sequencing of shorter regions from the same gene, like the V4-V5 region…
View article: Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon
Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon Open
Flavobacteriaceae spp. are key players in global biogeochemical cycling and are known for their versatile carbohydrate and peptide catabolism. However, it is currently unknown whether secondary metabolism traits underlie their broad range …
View article: Widespread occurrence of chitinase-encoding genes suggests the <i>Endozoicomonadaceae</i> family as a key player in chitin processing in the marine benthos
Widespread occurrence of chitinase-encoding genes suggests the <i>Endozoicomonadaceae</i> family as a key player in chitin processing in the marine benthos Open
Chitin is the most abundant natural polymer in the oceans, where it is primarily recycled by chitin-degrading microorganisms. Endozoicomonadaceae (Oceanospirillales) bacteria are prominent symbionts of sessile marine animals, particularly …
View article: Inter-comparison of marine microbiome sampling protocols
Inter-comparison of marine microbiome sampling protocols Open
Research on marine microbial communities is growing, but studies are hard to compare because of variation in seawater sampling protocols. To help researchers in the inter-comparison of studies that use different seawater sampling methodolo…
View article: Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon
Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon Open
Code and data for the article "Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon".
View article: Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon
Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon Open
Code and data for the article "Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon".
View article: The prokaryotic community of Chondrosia reniformis Nardo, 1847: from diversity to mercury detection
The prokaryotic community of Chondrosia reniformis Nardo, 1847: from diversity to mercury detection Open
Microbial communities inhabiting sponges are known to take part in many metabolic pathways, including nutrient cycles, and possibly also in the bioaccumulation of trace elements (TEs). Here, we used high-throughput, Illumina sequencing of …
View article: Marine Sponge and Octocoral-Associated Bacteria Show Versatile Secondary Metabolite Biosynthesis Potential and Antimicrobial Activities against Human Pathogens
Marine Sponge and Octocoral-Associated Bacteria Show Versatile Secondary Metabolite Biosynthesis Potential and Antimicrobial Activities against Human Pathogens Open
Marine microbiomes are prolific sources of bioactive natural products of potential pharmaceutical value. This study inspected two culture collections comprising 919 host-associated marine bacteria belonging to 55 genera and several thus-fa…
View article: Genome Sequencing Suggests Diverse Secondary Metabolism in Coral-Associated Aquimarina megaterium
Genome Sequencing Suggests Diverse Secondary Metabolism in Coral-Associated Aquimarina megaterium Open
We report here the genome sequences of three Aquimarina megaterium strains isolated from the octocoral Eunicella labiata . We reveal a coding potential for versatile carbon metabolism and biosynthesis of natural products belonging to the p…